Multiple sequence alignment - TraesCS5B01G499500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G499500 chr5B 100.000 3303 0 0 1 3303 665940706 665944008 0.000000e+00 6100
1 TraesCS5B01G499500 chr5B 91.011 445 36 3 2604 3045 665830441 665830884 6.100000e-167 597
2 TraesCS5B01G499500 chr5B 81.712 514 73 11 152 653 665961225 665961729 3.070000e-110 409
3 TraesCS5B01G499500 chr5B 84.459 148 23 0 2616 2763 665963575 665963722 2.660000e-31 147
4 TraesCS5B01G499500 chr5D 91.518 2582 131 20 1 2538 528764176 528766713 0.000000e+00 3474
5 TraesCS5B01G499500 chr5D 79.426 2197 374 38 33 2188 528805335 528807494 0.000000e+00 1482
6 TraesCS5B01G499500 chr5D 79.563 2016 338 37 63 2053 528753028 528754994 0.000000e+00 1373
7 TraesCS5B01G499500 chr5D 90.355 591 31 8 2538 3106 528767177 528767763 0.000000e+00 752
8 TraesCS5B01G499500 chr5D 78.061 196 27 9 2240 2435 528755277 528755456 3.480000e-20 110
9 TraesCS5B01G499500 chr6B 80.015 1321 239 14 883 2195 106512232 106513535 0.000000e+00 953
10 TraesCS5B01G499500 chr6B 78.990 614 88 18 253 827 106511585 106512196 6.690000e-102 381
11 TraesCS5B01G499500 chrUn 79.898 786 137 14 1417 2195 97785708 97786479 1.040000e-154 556
12 TraesCS5B01G499500 chrUn 79.058 616 84 22 253 827 97784586 97785197 6.690000e-102 381
13 TraesCS5B01G499500 chr1D 76.872 1055 173 36 253 1266 476568595 476567571 6.280000e-147 531
14 TraesCS5B01G499500 chr1D 86.395 147 20 0 145 291 476568736 476568590 9.490000e-36 161
15 TraesCS5B01G499500 chr1B 78.000 450 60 20 394 805 662836822 662836374 2.550000e-61 246


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G499500 chr5B 665940706 665944008 3302 False 6100.0 6100 100.0000 1 3303 1 chr5B.!!$F2 3302
1 TraesCS5B01G499500 chr5B 665961225 665963722 2497 False 278.0 409 83.0855 152 2763 2 chr5B.!!$F3 2611
2 TraesCS5B01G499500 chr5D 528764176 528767763 3587 False 2113.0 3474 90.9365 1 3106 2 chr5D.!!$F3 3105
3 TraesCS5B01G499500 chr5D 528805335 528807494 2159 False 1482.0 1482 79.4260 33 2188 1 chr5D.!!$F1 2155
4 TraesCS5B01G499500 chr5D 528753028 528755456 2428 False 741.5 1373 78.8120 63 2435 2 chr5D.!!$F2 2372
5 TraesCS5B01G499500 chr6B 106511585 106513535 1950 False 667.0 953 79.5025 253 2195 2 chr6B.!!$F1 1942
6 TraesCS5B01G499500 chrUn 97784586 97786479 1893 False 468.5 556 79.4780 253 2195 2 chrUn.!!$F1 1942
7 TraesCS5B01G499500 chr1D 476567571 476568736 1165 True 346.0 531 81.6335 145 1266 2 chr1D.!!$R1 1121

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
778 937 0.248907 GCATGCACATTGCTAGCCTG 60.249 55.0 14.21 12.33 45.31 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 3237 0.177141 CGGAGCCCGGAATAAGTGAA 59.823 55.0 0.73 0.0 44.15 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 50 7.500892 TGCCTTTTCTGTCTAGTTGTTAATGAA 59.499 33.333 0.00 0.00 0.00 2.57
46 51 8.017946 GCCTTTTCTGTCTAGTTGTTAATGAAG 58.982 37.037 0.00 0.00 0.00 3.02
47 52 9.273016 CCTTTTCTGTCTAGTTGTTAATGAAGA 57.727 33.333 0.00 0.00 0.00 2.87
86 91 3.845781 ATAGCATGAAGGTGTTCCGAT 57.154 42.857 0.00 0.00 39.05 4.18
89 94 2.489329 AGCATGAAGGTGTTCCGATTTG 59.511 45.455 0.00 0.00 39.05 2.32
125 130 6.613233 ACTATGTATACTATTGACGCAGAGC 58.387 40.000 4.17 0.00 0.00 4.09
180 185 1.410517 ACCTGGTACATGATCTCGCAG 59.589 52.381 0.00 0.00 38.20 5.18
322 366 4.966366 GCATTTTCATGATCGTAGCAACTC 59.034 41.667 0.00 0.00 31.07 3.01
466 513 3.338250 TTCATGGGGCCGGAAGCT 61.338 61.111 5.05 0.00 43.05 3.74
555 620 1.306642 ATCACGTCGCGGAAGACTCT 61.307 55.000 6.13 0.00 38.90 3.24
608 673 8.842358 TCATGGAACTCCGGTATTTAAATATC 57.158 34.615 11.00 9.57 39.43 1.63
667 807 3.740321 TCGGCAAATCAAAGTTTCATTGC 59.260 39.130 15.91 15.91 41.69 3.56
687 827 0.672342 CTGTATCGGTACCCTTCCCG 59.328 60.000 6.25 0.00 45.55 5.14
743 902 5.535753 AAGTTTTAGCAGCCTCAACAAAT 57.464 34.783 0.00 0.00 0.00 2.32
778 937 0.248907 GCATGCACATTGCTAGCCTG 60.249 55.000 14.21 12.33 45.31 4.85
837 1017 1.175983 GGATTGTTGCAACACGGGGA 61.176 55.000 31.17 17.16 38.92 4.81
848 1028 2.430367 ACGGGGAGTTTCCTGTGC 59.570 61.111 0.00 0.00 44.21 4.57
849 1029 2.742372 CGGGGAGTTTCCTGTGCG 60.742 66.667 0.00 0.00 36.57 5.34
850 1030 2.430367 GGGGAGTTTCCTGTGCGT 59.570 61.111 0.00 0.00 36.57 5.24
851 1031 1.966451 GGGGAGTTTCCTGTGCGTG 60.966 63.158 0.00 0.00 36.57 5.34
852 1032 2.617274 GGGAGTTTCCTGTGCGTGC 61.617 63.158 0.00 0.00 36.57 5.34
853 1033 1.891919 GGAGTTTCCTGTGCGTGCA 60.892 57.895 0.00 0.00 32.53 4.57
854 1034 1.571460 GAGTTTCCTGTGCGTGCAG 59.429 57.895 0.00 2.11 36.31 4.41
855 1035 0.880278 GAGTTTCCTGTGCGTGCAGA 60.880 55.000 9.40 0.00 38.70 4.26
856 1036 0.250467 AGTTTCCTGTGCGTGCAGAT 60.250 50.000 9.40 0.00 38.70 2.90
857 1037 0.593128 GTTTCCTGTGCGTGCAGATT 59.407 50.000 9.40 0.00 38.70 2.40
858 1038 1.001378 GTTTCCTGTGCGTGCAGATTT 60.001 47.619 9.40 0.00 38.70 2.17
859 1039 1.317613 TTCCTGTGCGTGCAGATTTT 58.682 45.000 9.40 0.00 38.70 1.82
860 1040 1.317613 TCCTGTGCGTGCAGATTTTT 58.682 45.000 9.40 0.00 38.70 1.94
886 1066 1.284657 GTGAGGACGTGCAGATGATG 58.715 55.000 10.52 0.00 0.00 3.07
978 1159 8.994429 ATCTTGTAAATGTGAAGTCTGTAGAG 57.006 34.615 0.00 0.00 0.00 2.43
990 1171 2.202810 GTAGAGGAGGCACGCAGC 60.203 66.667 0.00 0.00 44.65 5.25
1033 1214 4.940046 AGAGCATCGAAGAATTGACATTGT 59.060 37.500 0.00 0.00 43.58 2.71
1077 1258 2.482374 GAACACATGGCGCTGCTC 59.518 61.111 7.64 0.00 0.00 4.26
1104 1285 1.603802 CTAGTGCCACCAACAACTGTG 59.396 52.381 0.00 0.00 0.00 3.66
1109 1290 0.381801 CCACCAACAACTGTGCAGAC 59.618 55.000 6.17 0.00 0.00 3.51
1161 1342 6.942005 TCATATTTCCATACTGGGTTATGCAG 59.058 38.462 0.00 0.00 38.32 4.41
1230 1414 2.358615 TGCAGCAGCCTACCAACG 60.359 61.111 0.00 0.00 41.13 4.10
1253 1437 1.619827 CGTCCAACTACCCAACCTACA 59.380 52.381 0.00 0.00 0.00 2.74
1280 1464 9.941664 CAAGATTTTTCTTGGCTACATGTATAG 57.058 33.333 5.91 0.00 42.34 1.31
1510 1694 1.671901 CTCCTCTTCTCCTCCCGTGC 61.672 65.000 0.00 0.00 0.00 5.34
1512 1696 1.216710 CTCTTCTCCTCCCGTGCAC 59.783 63.158 6.82 6.82 0.00 4.57
1628 1812 4.518590 CGATGATCTGACTATCTCACCACT 59.481 45.833 0.00 0.00 0.00 4.00
1630 1814 4.604156 TGATCTGACTATCTCACCACTGT 58.396 43.478 0.00 0.00 0.00 3.55
1681 1865 3.118112 ACTCTCCCTCGAATGCATTGAAT 60.118 43.478 18.59 0.00 0.00 2.57
1750 1934 6.375174 ACAGCTCAACTTAATATGCATGAACA 59.625 34.615 10.16 0.00 0.00 3.18
1760 1944 2.198827 TGCATGAACAACCTACAGGG 57.801 50.000 0.00 0.00 40.27 4.45
1767 1951 3.396276 TGAACAACCTACAGGGATTGGAA 59.604 43.478 0.00 0.00 40.27 3.53
1807 1991 3.282021 ACACAGTTGCAATCACTGAGTT 58.718 40.909 21.00 4.53 32.90 3.01
1813 1997 3.631145 TGCAATCACTGAGTTTGAAGC 57.369 42.857 1.41 0.00 0.00 3.86
1831 2015 2.232239 GCACTGTAATGCGTTGACAG 57.768 50.000 18.66 18.66 44.98 3.51
1860 2044 2.237392 GCAATGGTTAGGAGGACTCACT 59.763 50.000 1.32 0.00 0.00 3.41
1870 2054 2.421619 GAGGACTCACTTTGCTCAAGG 58.578 52.381 0.00 0.00 36.72 3.61
1935 2417 3.450457 AGAGCTTACTCATCAACCTCCAG 59.550 47.826 0.00 0.00 46.09 3.86
1949 2431 6.552008 TCAACCTCCAGGAACTTCATATTTT 58.448 36.000 0.00 0.00 34.60 1.82
2004 2560 3.999663 CAGAGGTGAACCAGATGAAACTC 59.000 47.826 1.62 0.00 38.89 3.01
2059 2620 5.856126 TTGCTCTTATGTTTTACCGACTG 57.144 39.130 0.00 0.00 0.00 3.51
2193 2901 5.589050 GGGGTAAACCAGATTAGCTTGTTAG 59.411 44.000 0.00 0.00 42.91 2.34
2195 2903 7.054751 GGGTAAACCAGATTAGCTTGTTAGAT 58.945 38.462 0.00 0.00 39.85 1.98
2229 2955 9.679661 AAAAACAATGTTACCTTCCAGAAAATT 57.320 25.926 0.00 0.00 0.00 1.82
2230 2956 8.661352 AAACAATGTTACCTTCCAGAAAATTG 57.339 30.769 0.00 0.00 0.00 2.32
2235 2961 5.008217 TGTTACCTTCCAGAAAATTGTCGTG 59.992 40.000 0.00 0.00 0.00 4.35
2249 2975 1.066303 TGTCGTGCCCATGTGTTTTTC 59.934 47.619 0.00 0.00 0.00 2.29
2262 2988 7.222611 CCCATGTGTTTTTCTAACAAGAAACAG 59.777 37.037 0.19 0.00 41.16 3.16
2389 3149 1.191489 TTCTGACGCCATGGTGGAGA 61.191 55.000 28.34 23.67 39.92 3.71
2394 3154 1.002134 CGCCATGGTGGAGACCTTT 60.002 57.895 18.06 0.00 39.92 3.11
2460 3236 9.634021 TTTTTGCCTTTTATTTCCCATAAACTT 57.366 25.926 0.00 0.00 0.00 2.66
2461 3237 9.634021 TTTTGCCTTTTATTTCCCATAAACTTT 57.366 25.926 0.00 0.00 0.00 2.66
2463 3239 8.840833 TGCCTTTTATTTCCCATAAACTTTTC 57.159 30.769 0.00 0.00 0.00 2.29
2464 3240 8.432805 TGCCTTTTATTTCCCATAAACTTTTCA 58.567 29.630 0.00 0.00 0.00 2.69
2465 3241 8.717821 GCCTTTTATTTCCCATAAACTTTTCAC 58.282 33.333 0.00 0.00 0.00 3.18
2490 3268 4.415783 GGGCTCCGATGGTTTTGT 57.584 55.556 0.00 0.00 0.00 2.83
2492 3270 0.608035 GGGCTCCGATGGTTTTGTGA 60.608 55.000 0.00 0.00 0.00 3.58
2493 3271 0.804989 GGCTCCGATGGTTTTGTGAG 59.195 55.000 0.00 0.00 0.00 3.51
2495 3273 1.522668 CTCCGATGGTTTTGTGAGCA 58.477 50.000 0.00 0.00 0.00 4.26
2496 3274 1.197721 CTCCGATGGTTTTGTGAGCAC 59.802 52.381 0.00 0.00 0.00 4.40
2497 3275 1.202758 TCCGATGGTTTTGTGAGCACT 60.203 47.619 1.99 0.00 0.00 4.40
2511 3289 6.072112 TGTGAGCACTTTCACTTTATTTCC 57.928 37.500 7.56 0.00 46.00 3.13
2524 3302 7.695055 TCACTTTATTTCCCCTTCTGTATTGA 58.305 34.615 0.00 0.00 0.00 2.57
2570 3816 4.398988 TGAGTGACTTCAGCAACACAAAAT 59.601 37.500 0.00 0.00 35.97 1.82
2606 3859 6.864342 ACAGTATTCTACTACGAGCACATTT 58.136 36.000 0.00 0.00 37.23 2.32
2609 3862 8.129840 CAGTATTCTACTACGAGCACATTTACT 58.870 37.037 0.00 0.00 37.23 2.24
2617 3900 3.244078 ACGAGCACATTTACTCTGGTCAA 60.244 43.478 0.00 0.00 32.98 3.18
2636 3919 1.961277 CTTTCGACGTTGCTGCCCT 60.961 57.895 0.00 0.00 0.00 5.19
2644 3927 1.148157 CGTTGCTGCCCTATGACTCG 61.148 60.000 0.00 0.00 0.00 4.18
2704 3987 3.490933 GCTTCTGTATACCGTCTCATGCA 60.491 47.826 0.00 0.00 0.00 3.96
2779 4062 4.844998 ATGTATGAGGTCTCTGACATCG 57.155 45.455 7.65 0.00 44.84 3.84
2781 4064 0.749649 ATGAGGTCTCTGACATCGCC 59.250 55.000 7.65 0.00 44.84 5.54
2786 4069 0.454600 GTCTCTGACATCGCCGGTAA 59.545 55.000 1.90 0.00 32.09 2.85
2822 4107 9.261180 AGTATTAGTTCAATGTGGTATCGATTG 57.739 33.333 1.71 0.00 0.00 2.67
2828 4113 0.529773 TGTGGTATCGATTGCTCGCC 60.530 55.000 1.71 0.00 44.65 5.54
2859 4144 2.503765 TCGTGCTCTTATTTCCCCATGA 59.496 45.455 0.00 0.00 0.00 3.07
2960 4246 4.703093 TGTGCAATCATGACACTGATCATT 59.297 37.500 14.06 0.00 37.20 2.57
2961 4247 5.881443 TGTGCAATCATGACACTGATCATTA 59.119 36.000 14.06 0.00 37.20 1.90
2962 4248 6.544564 TGTGCAATCATGACACTGATCATTAT 59.455 34.615 14.06 0.00 37.20 1.28
2986 4282 7.837202 TCCAAATATAAGACGTGTTTGTAGG 57.163 36.000 2.22 0.00 0.00 3.18
2998 4294 7.769044 AGACGTGTTTGTAGGCTAATTTGATAT 59.231 33.333 0.00 0.00 0.00 1.63
3006 4302 5.248380 AGGCTAATTTGATATGGAGGGAC 57.752 43.478 0.00 0.00 0.00 4.46
3056 4352 7.784633 TTTCATTAGATGTACATTGCATCGA 57.215 32.000 10.30 0.65 45.25 3.59
3073 4369 6.599437 TGCATCGAGCTACTTTCTTAAAAAC 58.401 36.000 8.07 0.00 45.94 2.43
3079 4377 7.279313 TCGAGCTACTTTCTTAAAAACACACTT 59.721 33.333 0.00 0.00 0.00 3.16
3082 4380 8.618677 AGCTACTTTCTTAAAAACACACTTACC 58.381 33.333 0.00 0.00 0.00 2.85
3087 4385 7.995463 TTCTTAAAAACACACTTACCAATGC 57.005 32.000 0.00 0.00 0.00 3.56
3093 4391 4.202245 ACACACTTACCAATGCGACTAT 57.798 40.909 0.00 0.00 0.00 2.12
3095 4393 4.180817 CACACTTACCAATGCGACTATGA 58.819 43.478 0.00 0.00 0.00 2.15
3099 4397 2.604046 ACCAATGCGACTATGAGGTC 57.396 50.000 0.00 0.00 0.00 3.85
3110 4408 5.098218 GACTATGAGGTCGCACTAGTAAG 57.902 47.826 0.00 0.00 0.00 2.34
3111 4409 3.884091 ACTATGAGGTCGCACTAGTAAGG 59.116 47.826 0.00 0.00 0.00 2.69
3112 4410 2.211250 TGAGGTCGCACTAGTAAGGT 57.789 50.000 0.00 0.00 0.00 3.50
3113 4411 3.354948 TGAGGTCGCACTAGTAAGGTA 57.645 47.619 0.00 0.00 0.00 3.08
3114 4412 3.012518 TGAGGTCGCACTAGTAAGGTAC 58.987 50.000 0.00 0.00 0.00 3.34
3115 4413 2.357323 GAGGTCGCACTAGTAAGGTACC 59.643 54.545 2.73 2.73 0.00 3.34
3116 4414 1.406898 GGTCGCACTAGTAAGGTACCC 59.593 57.143 8.74 0.00 0.00 3.69
3117 4415 1.064654 GTCGCACTAGTAAGGTACCCG 59.935 57.143 8.74 1.35 0.00 5.28
3118 4416 1.098050 CGCACTAGTAAGGTACCCGT 58.902 55.000 8.74 0.00 0.00 5.28
3119 4417 1.202222 CGCACTAGTAAGGTACCCGTG 60.202 57.143 8.74 7.83 34.46 4.94
3120 4418 1.470458 GCACTAGTAAGGTACCCGTGC 60.470 57.143 8.74 13.58 43.24 5.34
3121 4419 1.820519 CACTAGTAAGGTACCCGTGCA 59.179 52.381 8.74 0.00 0.00 4.57
3122 4420 2.429610 CACTAGTAAGGTACCCGTGCAT 59.570 50.000 8.74 0.00 0.00 3.96
3123 4421 3.633525 CACTAGTAAGGTACCCGTGCATA 59.366 47.826 8.74 0.00 0.00 3.14
3124 4422 4.280174 CACTAGTAAGGTACCCGTGCATAT 59.720 45.833 8.74 0.00 0.00 1.78
3125 4423 4.897670 ACTAGTAAGGTACCCGTGCATATT 59.102 41.667 8.74 0.00 0.00 1.28
3126 4424 6.016024 CACTAGTAAGGTACCCGTGCATATTA 60.016 42.308 8.74 0.00 0.00 0.98
3127 4425 5.205759 AGTAAGGTACCCGTGCATATTAC 57.794 43.478 8.74 8.19 0.00 1.89
3128 4426 3.480505 AAGGTACCCGTGCATATTACC 57.519 47.619 8.74 8.12 33.63 2.85
3129 4427 1.695788 AGGTACCCGTGCATATTACCC 59.304 52.381 8.74 0.16 33.89 3.69
3130 4428 1.417145 GGTACCCGTGCATATTACCCA 59.583 52.381 0.00 0.00 0.00 4.51
3131 4429 2.486918 GTACCCGTGCATATTACCCAC 58.513 52.381 0.00 0.00 0.00 4.61
3132 4430 0.913205 ACCCGTGCATATTACCCACA 59.087 50.000 0.00 0.00 0.00 4.17
3133 4431 1.282447 ACCCGTGCATATTACCCACAA 59.718 47.619 0.00 0.00 0.00 3.33
3134 4432 2.291024 ACCCGTGCATATTACCCACAAA 60.291 45.455 0.00 0.00 0.00 2.83
3135 4433 2.755655 CCCGTGCATATTACCCACAAAA 59.244 45.455 0.00 0.00 0.00 2.44
3136 4434 3.383185 CCCGTGCATATTACCCACAAAAT 59.617 43.478 0.00 0.00 0.00 1.82
3137 4435 4.580995 CCCGTGCATATTACCCACAAAATA 59.419 41.667 0.00 0.00 0.00 1.40
3138 4436 5.506649 CCCGTGCATATTACCCACAAAATAC 60.507 44.000 0.00 0.00 0.00 1.89
3139 4437 5.506649 CCGTGCATATTACCCACAAAATACC 60.507 44.000 0.00 0.00 0.00 2.73
3140 4438 5.066634 CGTGCATATTACCCACAAAATACCA 59.933 40.000 0.00 0.00 0.00 3.25
3141 4439 6.238897 CGTGCATATTACCCACAAAATACCAT 60.239 38.462 0.00 0.00 0.00 3.55
3142 4440 7.145323 GTGCATATTACCCACAAAATACCATC 58.855 38.462 0.00 0.00 0.00 3.51
3143 4441 6.836007 TGCATATTACCCACAAAATACCATCA 59.164 34.615 0.00 0.00 0.00 3.07
3144 4442 7.145323 GCATATTACCCACAAAATACCATCAC 58.855 38.462 0.00 0.00 0.00 3.06
3145 4443 7.657336 CATATTACCCACAAAATACCATCACC 58.343 38.462 0.00 0.00 0.00 4.02
3146 4444 3.534357 ACCCACAAAATACCATCACCA 57.466 42.857 0.00 0.00 0.00 4.17
3147 4445 4.059773 ACCCACAAAATACCATCACCAT 57.940 40.909 0.00 0.00 0.00 3.55
3148 4446 4.424842 ACCCACAAAATACCATCACCATT 58.575 39.130 0.00 0.00 0.00 3.16
3149 4447 4.466015 ACCCACAAAATACCATCACCATTC 59.534 41.667 0.00 0.00 0.00 2.67
3150 4448 4.465660 CCCACAAAATACCATCACCATTCA 59.534 41.667 0.00 0.00 0.00 2.57
3151 4449 5.394443 CCCACAAAATACCATCACCATTCAG 60.394 44.000 0.00 0.00 0.00 3.02
3152 4450 5.104374 CACAAAATACCATCACCATTCAGC 58.896 41.667 0.00 0.00 0.00 4.26
3153 4451 4.771577 ACAAAATACCATCACCATTCAGCA 59.228 37.500 0.00 0.00 0.00 4.41
3154 4452 5.245751 ACAAAATACCATCACCATTCAGCAA 59.754 36.000 0.00 0.00 0.00 3.91
3155 4453 6.070653 ACAAAATACCATCACCATTCAGCAAT 60.071 34.615 0.00 0.00 0.00 3.56
3156 4454 7.123997 ACAAAATACCATCACCATTCAGCAATA 59.876 33.333 0.00 0.00 0.00 1.90
3157 4455 7.844493 AAATACCATCACCATTCAGCAATAT 57.156 32.000 0.00 0.00 0.00 1.28
3158 4456 7.844493 AATACCATCACCATTCAGCAATATT 57.156 32.000 0.00 0.00 0.00 1.28
3159 4457 7.844493 ATACCATCACCATTCAGCAATATTT 57.156 32.000 0.00 0.00 0.00 1.40
3160 4458 8.938801 ATACCATCACCATTCAGCAATATTTA 57.061 30.769 0.00 0.00 0.00 1.40
3161 4459 7.042797 ACCATCACCATTCAGCAATATTTAC 57.957 36.000 0.00 0.00 0.00 2.01
3162 4460 6.606796 ACCATCACCATTCAGCAATATTTACA 59.393 34.615 0.00 0.00 0.00 2.41
3163 4461 7.143340 CCATCACCATTCAGCAATATTTACAG 58.857 38.462 0.00 0.00 0.00 2.74
3164 4462 7.013559 CCATCACCATTCAGCAATATTTACAGA 59.986 37.037 0.00 0.00 0.00 3.41
3165 4463 7.320443 TCACCATTCAGCAATATTTACAGAC 57.680 36.000 0.00 0.00 0.00 3.51
3166 4464 7.112122 TCACCATTCAGCAATATTTACAGACT 58.888 34.615 0.00 0.00 0.00 3.24
3167 4465 7.280876 TCACCATTCAGCAATATTTACAGACTC 59.719 37.037 0.00 0.00 0.00 3.36
3168 4466 7.281774 CACCATTCAGCAATATTTACAGACTCT 59.718 37.037 0.00 0.00 0.00 3.24
3169 4467 8.486210 ACCATTCAGCAATATTTACAGACTCTA 58.514 33.333 0.00 0.00 0.00 2.43
3170 4468 9.499479 CCATTCAGCAATATTTACAGACTCTAT 57.501 33.333 0.00 0.00 0.00 1.98
3186 4484 7.863375 ACAGACTCTATATTGTACAAATCGAGC 59.137 37.037 13.23 12.45 0.00 5.03
3187 4485 8.079203 CAGACTCTATATTGTACAAATCGAGCT 58.921 37.037 13.23 13.93 0.00 4.09
3188 4486 8.634444 AGACTCTATATTGTACAAATCGAGCTT 58.366 33.333 13.23 7.49 0.00 3.74
3189 4487 8.804688 ACTCTATATTGTACAAATCGAGCTTC 57.195 34.615 13.23 0.00 0.00 3.86
3190 4488 8.414003 ACTCTATATTGTACAAATCGAGCTTCA 58.586 33.333 13.23 0.00 0.00 3.02
3191 4489 9.416794 CTCTATATTGTACAAATCGAGCTTCAT 57.583 33.333 13.23 0.00 0.00 2.57
3192 4490 9.764363 TCTATATTGTACAAATCGAGCTTCATT 57.236 29.630 13.23 0.00 0.00 2.57
3195 4493 6.552859 TTGTACAAATCGAGCTTCATTTGA 57.447 33.333 26.34 14.06 40.89 2.69
3196 4494 6.741992 TGTACAAATCGAGCTTCATTTGAT 57.258 33.333 26.34 17.25 40.89 2.57
3197 4495 7.144722 TGTACAAATCGAGCTTCATTTGATT 57.855 32.000 26.34 14.41 40.89 2.57
3198 4496 7.592938 TGTACAAATCGAGCTTCATTTGATTT 58.407 30.769 26.34 12.86 40.89 2.17
3199 4497 8.081633 TGTACAAATCGAGCTTCATTTGATTTT 58.918 29.630 26.34 13.67 40.89 1.82
3200 4498 9.554724 GTACAAATCGAGCTTCATTTGATTTTA 57.445 29.630 26.34 12.98 40.89 1.52
3202 4500 9.294030 ACAAATCGAGCTTCATTTGATTTTATC 57.706 29.630 26.34 0.00 40.89 1.75
3203 4501 8.466799 CAAATCGAGCTTCATTTGATTTTATCG 58.533 33.333 19.51 0.97 40.89 2.92
3204 4502 6.902224 TCGAGCTTCATTTGATTTTATCGA 57.098 33.333 0.00 0.00 33.55 3.59
3205 4503 7.482654 TCGAGCTTCATTTGATTTTATCGAT 57.517 32.000 2.16 2.16 31.28 3.59
3206 4504 8.587952 TCGAGCTTCATTTGATTTTATCGATA 57.412 30.769 0.00 0.00 31.28 2.92
3207 4505 9.040939 TCGAGCTTCATTTGATTTTATCGATAA 57.959 29.630 13.85 13.85 31.28 1.75
3208 4506 9.310971 CGAGCTTCATTTGATTTTATCGATAAG 57.689 33.333 16.89 5.08 0.00 1.73
3223 4521 8.981724 TTATCGATAAGAAATAGATGGTTCGG 57.018 34.615 13.85 0.00 0.00 4.30
3224 4522 6.401047 TCGATAAGAAATAGATGGTTCGGT 57.599 37.500 0.00 0.00 0.00 4.69
3225 4523 6.812998 TCGATAAGAAATAGATGGTTCGGTT 58.187 36.000 0.00 0.00 0.00 4.44
3226 4524 7.944061 TCGATAAGAAATAGATGGTTCGGTTA 58.056 34.615 0.00 0.00 0.00 2.85
3227 4525 8.080417 TCGATAAGAAATAGATGGTTCGGTTAG 58.920 37.037 0.00 0.00 0.00 2.34
3228 4526 7.328737 CGATAAGAAATAGATGGTTCGGTTAGG 59.671 40.741 0.00 0.00 0.00 2.69
3229 4527 5.952347 AGAAATAGATGGTTCGGTTAGGT 57.048 39.130 0.00 0.00 0.00 3.08
3230 4528 6.309389 AGAAATAGATGGTTCGGTTAGGTT 57.691 37.500 0.00 0.00 0.00 3.50
3231 4529 6.113411 AGAAATAGATGGTTCGGTTAGGTTG 58.887 40.000 0.00 0.00 0.00 3.77
3232 4530 5.431179 AATAGATGGTTCGGTTAGGTTGT 57.569 39.130 0.00 0.00 0.00 3.32
3233 4531 3.782656 AGATGGTTCGGTTAGGTTGTT 57.217 42.857 0.00 0.00 0.00 2.83
3234 4532 3.408634 AGATGGTTCGGTTAGGTTGTTG 58.591 45.455 0.00 0.00 0.00 3.33
3235 4533 3.071892 AGATGGTTCGGTTAGGTTGTTGA 59.928 43.478 0.00 0.00 0.00 3.18
3236 4534 3.278668 TGGTTCGGTTAGGTTGTTGAA 57.721 42.857 0.00 0.00 0.00 2.69
3237 4535 3.207778 TGGTTCGGTTAGGTTGTTGAAG 58.792 45.455 0.00 0.00 0.00 3.02
3238 4536 3.208594 GGTTCGGTTAGGTTGTTGAAGT 58.791 45.455 0.00 0.00 0.00 3.01
3239 4537 3.249320 GGTTCGGTTAGGTTGTTGAAGTC 59.751 47.826 0.00 0.00 0.00 3.01
3240 4538 4.124970 GTTCGGTTAGGTTGTTGAAGTCT 58.875 43.478 0.00 0.00 0.00 3.24
3241 4539 5.291971 GTTCGGTTAGGTTGTTGAAGTCTA 58.708 41.667 0.00 0.00 0.00 2.59
3242 4540 5.130292 TCGGTTAGGTTGTTGAAGTCTAG 57.870 43.478 0.00 0.00 0.00 2.43
3243 4541 4.828939 TCGGTTAGGTTGTTGAAGTCTAGA 59.171 41.667 0.00 0.00 0.00 2.43
3244 4542 5.479375 TCGGTTAGGTTGTTGAAGTCTAGAT 59.521 40.000 0.00 0.00 0.00 1.98
3245 4543 5.805994 CGGTTAGGTTGTTGAAGTCTAGATC 59.194 44.000 0.00 0.00 0.00 2.75
3246 4544 6.107343 GGTTAGGTTGTTGAAGTCTAGATCC 58.893 44.000 0.00 0.00 0.00 3.36
3247 4545 4.828072 AGGTTGTTGAAGTCTAGATCCC 57.172 45.455 0.00 0.00 0.00 3.85
3248 4546 4.430441 AGGTTGTTGAAGTCTAGATCCCT 58.570 43.478 0.00 0.00 0.00 4.20
3249 4547 5.590818 AGGTTGTTGAAGTCTAGATCCCTA 58.409 41.667 0.00 0.00 0.00 3.53
3250 4548 6.206042 AGGTTGTTGAAGTCTAGATCCCTAT 58.794 40.000 0.00 0.00 0.00 2.57
3251 4549 6.098982 AGGTTGTTGAAGTCTAGATCCCTATG 59.901 42.308 0.00 0.00 0.00 2.23
3252 4550 6.098409 GGTTGTTGAAGTCTAGATCCCTATGA 59.902 42.308 0.00 0.00 0.00 2.15
3253 4551 6.716934 TGTTGAAGTCTAGATCCCTATGAC 57.283 41.667 0.00 0.00 0.00 3.06
3254 4552 6.194967 TGTTGAAGTCTAGATCCCTATGACA 58.805 40.000 0.00 0.00 31.42 3.58
3255 4553 6.096987 TGTTGAAGTCTAGATCCCTATGACAC 59.903 42.308 0.00 0.00 31.42 3.67
3256 4554 5.141182 TGAAGTCTAGATCCCTATGACACC 58.859 45.833 0.00 0.00 31.42 4.16
3257 4555 5.103473 TGAAGTCTAGATCCCTATGACACCT 60.103 44.000 0.00 0.00 31.42 4.00
3258 4556 5.411103 AGTCTAGATCCCTATGACACCTT 57.589 43.478 0.00 0.00 31.42 3.50
3259 4557 5.390387 AGTCTAGATCCCTATGACACCTTC 58.610 45.833 0.00 0.00 31.42 3.46
3260 4558 5.135362 AGTCTAGATCCCTATGACACCTTCT 59.865 44.000 0.00 0.00 31.42 2.85
3261 4559 6.333168 AGTCTAGATCCCTATGACACCTTCTA 59.667 42.308 0.00 0.00 31.42 2.10
3262 4560 6.431852 GTCTAGATCCCTATGACACCTTCTAC 59.568 46.154 0.00 0.00 0.00 2.59
3263 4561 5.144159 AGATCCCTATGACACCTTCTACA 57.856 43.478 0.00 0.00 0.00 2.74
3264 4562 5.144100 AGATCCCTATGACACCTTCTACAG 58.856 45.833 0.00 0.00 0.00 2.74
3265 4563 4.603094 TCCCTATGACACCTTCTACAGA 57.397 45.455 0.00 0.00 0.00 3.41
3266 4564 4.279145 TCCCTATGACACCTTCTACAGAC 58.721 47.826 0.00 0.00 0.00 3.51
3267 4565 3.385111 CCCTATGACACCTTCTACAGACC 59.615 52.174 0.00 0.00 0.00 3.85
3268 4566 3.066900 CCTATGACACCTTCTACAGACCG 59.933 52.174 0.00 0.00 0.00 4.79
3269 4567 1.254026 TGACACCTTCTACAGACCGG 58.746 55.000 0.00 0.00 0.00 5.28
3270 4568 1.202964 TGACACCTTCTACAGACCGGA 60.203 52.381 9.46 0.00 0.00 5.14
3271 4569 2.100989 GACACCTTCTACAGACCGGAT 58.899 52.381 9.46 0.00 0.00 4.18
3272 4570 2.099427 GACACCTTCTACAGACCGGATC 59.901 54.545 9.46 1.42 0.00 3.36
3273 4571 1.409427 CACCTTCTACAGACCGGATCC 59.591 57.143 9.46 0.00 0.00 3.36
3274 4572 1.288335 ACCTTCTACAGACCGGATCCT 59.712 52.381 9.46 0.00 0.00 3.24
3275 4573 2.512896 ACCTTCTACAGACCGGATCCTA 59.487 50.000 9.46 0.00 0.00 2.94
3276 4574 3.140519 ACCTTCTACAGACCGGATCCTAT 59.859 47.826 9.46 0.00 0.00 2.57
3277 4575 3.759618 CCTTCTACAGACCGGATCCTATC 59.240 52.174 9.46 7.10 0.00 2.08
3278 4576 4.399219 CTTCTACAGACCGGATCCTATCA 58.601 47.826 9.46 0.00 0.00 2.15
3279 4577 4.448720 TCTACAGACCGGATCCTATCAA 57.551 45.455 9.46 0.00 0.00 2.57
3280 4578 4.142790 TCTACAGACCGGATCCTATCAAC 58.857 47.826 9.46 0.00 0.00 3.18
3281 4579 2.040178 ACAGACCGGATCCTATCAACC 58.960 52.381 9.46 0.00 0.00 3.77
3282 4580 1.344763 CAGACCGGATCCTATCAACCC 59.655 57.143 9.46 0.00 0.00 4.11
3283 4581 0.685660 GACCGGATCCTATCAACCCC 59.314 60.000 9.46 0.00 0.00 4.95
3284 4582 0.030501 ACCGGATCCTATCAACCCCA 60.031 55.000 9.46 0.00 0.00 4.96
3285 4583 1.136828 CCGGATCCTATCAACCCCAA 58.863 55.000 10.75 0.00 0.00 4.12
3286 4584 1.705186 CCGGATCCTATCAACCCCAAT 59.295 52.381 10.75 0.00 0.00 3.16
3287 4585 2.290323 CCGGATCCTATCAACCCCAATC 60.290 54.545 10.75 0.00 0.00 2.67
3288 4586 2.371841 CGGATCCTATCAACCCCAATCA 59.628 50.000 10.75 0.00 0.00 2.57
3289 4587 3.009473 CGGATCCTATCAACCCCAATCAT 59.991 47.826 10.75 0.00 0.00 2.45
3290 4588 4.338879 GGATCCTATCAACCCCAATCATG 58.661 47.826 3.84 0.00 0.00 3.07
3292 4590 2.158475 TCCTATCAACCCCAATCATGGC 60.158 50.000 0.00 0.00 46.09 4.40
3293 4591 2.242043 CTATCAACCCCAATCATGGCC 58.758 52.381 0.00 0.00 46.09 5.36
3294 4592 0.339162 ATCAACCCCAATCATGGCCA 59.661 50.000 8.56 8.56 46.09 5.36
3295 4593 0.339162 TCAACCCCAATCATGGCCAT 59.661 50.000 14.09 14.09 46.09 4.40
3296 4594 0.466543 CAACCCCAATCATGGCCATG 59.533 55.000 35.76 35.76 46.09 3.66
3297 4595 0.691748 AACCCCAATCATGGCCATGG 60.692 55.000 38.81 27.55 46.09 3.66
3298 4596 1.233659 CCCCAATCATGGCCATGGA 59.766 57.895 38.81 27.30 46.09 3.41
3299 4597 1.117142 CCCCAATCATGGCCATGGAC 61.117 60.000 38.81 15.32 46.09 4.02
3300 4598 0.105862 CCCAATCATGGCCATGGACT 60.106 55.000 38.81 23.88 46.09 3.85
3301 4599 1.690209 CCCAATCATGGCCATGGACTT 60.690 52.381 38.81 27.37 46.09 3.01
3302 4600 1.411246 CCAATCATGGCCATGGACTTG 59.589 52.381 38.81 33.51 40.58 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 7.435068 TCATTAACAACTAGACAGAAAAGGC 57.565 36.000 0.00 0.00 0.00 4.35
125 130 6.073980 CCAAGAATTCAGTTTCAACTTGCATG 60.074 38.462 8.44 0.00 37.08 4.06
180 185 0.465705 TCATCGGCCAGAACAGATCC 59.534 55.000 2.24 0.00 0.00 3.36
322 366 1.718396 TGCTTCACGATCAAGCTGAG 58.282 50.000 15.06 0.00 45.59 3.35
468 515 1.337823 CCTTGTAGACTCCCACCGTTG 60.338 57.143 0.00 0.00 0.00 4.10
555 620 2.642311 TCATGACCTTTGGCAGTCCTAA 59.358 45.455 0.00 0.00 31.76 2.69
608 673 6.721571 AAATAATAACCGTGACAGTGTGAG 57.278 37.500 0.00 0.00 0.00 3.51
687 827 9.132521 CACAAAAACAATAGTCATTCCAAGATC 57.867 33.333 0.00 0.00 0.00 2.75
837 1017 0.250467 ATCTGCACGCACAGGAAACT 60.250 50.000 5.53 0.00 46.44 2.66
862 1042 2.031258 TCTGCACGTCCTCACAAAAA 57.969 45.000 0.00 0.00 0.00 1.94
863 1043 1.872952 CATCTGCACGTCCTCACAAAA 59.127 47.619 0.00 0.00 0.00 2.44
864 1044 1.069978 TCATCTGCACGTCCTCACAAA 59.930 47.619 0.00 0.00 0.00 2.83
865 1045 0.678950 TCATCTGCACGTCCTCACAA 59.321 50.000 0.00 0.00 0.00 3.33
866 1046 0.897621 ATCATCTGCACGTCCTCACA 59.102 50.000 0.00 0.00 0.00 3.58
867 1047 1.284657 CATCATCTGCACGTCCTCAC 58.715 55.000 0.00 0.00 0.00 3.51
868 1048 0.176449 CCATCATCTGCACGTCCTCA 59.824 55.000 0.00 0.00 0.00 3.86
869 1049 0.176680 ACCATCATCTGCACGTCCTC 59.823 55.000 0.00 0.00 0.00 3.71
870 1050 0.107993 CACCATCATCTGCACGTCCT 60.108 55.000 0.00 0.00 0.00 3.85
871 1051 0.108186 TCACCATCATCTGCACGTCC 60.108 55.000 0.00 0.00 0.00 4.79
872 1052 1.725641 TTCACCATCATCTGCACGTC 58.274 50.000 0.00 0.00 0.00 4.34
873 1053 2.093288 AGATTCACCATCATCTGCACGT 60.093 45.455 0.00 0.00 33.75 4.49
886 1066 1.742761 TTGCTGCTGCTAGATTCACC 58.257 50.000 17.00 0.00 40.48 4.02
911 1091 5.105635 TGAGGATTTGCATGCTTAAGAAAGG 60.106 40.000 20.33 0.00 29.51 3.11
978 1159 2.182842 CCTTATGCTGCGTGCCTCC 61.183 63.158 4.25 0.00 42.00 4.30
990 1171 6.095377 GCTCTGTTTTTCCATCAACCTTATG 58.905 40.000 0.00 0.00 0.00 1.90
1077 1258 1.537202 GTTGGTGGCACTAGCTCTTTG 59.463 52.381 18.45 0.00 41.70 2.77
1109 1290 9.801873 CACCCTTGTAACCAAATATATTCAAAG 57.198 33.333 0.00 0.00 0.00 2.77
1230 1414 0.672711 GGTTGGGTAGTTGGACGAGC 60.673 60.000 0.00 0.00 0.00 5.03
1253 1437 6.655078 ACATGTAGCCAAGAAAAATCTTGT 57.345 33.333 15.25 3.24 43.99 3.16
1280 1464 2.755103 CCTGTGGTAAATTCTTCCAGGC 59.245 50.000 0.00 0.00 32.42 4.85
1392 1576 1.775459 ACAGCTCTAGGAGGATACGGA 59.225 52.381 0.00 0.00 46.39 4.69
1397 1581 1.118838 GTGCACAGCTCTAGGAGGAT 58.881 55.000 13.17 0.00 0.00 3.24
1510 1694 5.573146 GGACTTCTCAACTTTCAGTTTGTG 58.427 41.667 0.00 0.00 36.03 3.33
1512 1696 4.570772 TCGGACTTCTCAACTTTCAGTTTG 59.429 41.667 0.00 0.00 36.03 2.93
1681 1865 5.299148 CAACCATTCTGGCAGAATTTTCAA 58.701 37.500 34.13 12.35 41.90 2.69
1720 1904 5.817296 TGCATATTAAGTTGAGCTGTCGAAT 59.183 36.000 0.00 0.00 0.00 3.34
1750 1934 5.077564 GTTCTTTTCCAATCCCTGTAGGTT 58.922 41.667 0.00 0.00 36.75 3.50
1760 1944 6.218746 AGTTGCTTCATGTTCTTTTCCAATC 58.781 36.000 0.00 0.00 0.00 2.67
1767 1951 6.095440 ACTGTGTAAGTTGCTTCATGTTCTTT 59.905 34.615 0.00 0.00 34.57 2.52
1807 1991 2.875317 TCAACGCATTACAGTGCTTCAA 59.125 40.909 0.00 0.00 42.88 2.69
1813 1997 1.530720 TGCTGTCAACGCATTACAGTG 59.469 47.619 0.00 0.00 42.10 3.66
1831 2015 1.137404 CTAACCATTGCGGCAGTGC 59.863 57.895 18.81 6.55 39.03 4.40
1870 2054 3.371168 TGCAAAAACGAATCTCAAGTGC 58.629 40.909 0.00 0.00 0.00 4.40
1911 2389 3.704061 GGAGGTTGATGAGTAAGCTCTCT 59.296 47.826 14.21 0.00 46.46 3.10
1935 2417 4.142160 GGGCAGTCCAAAATATGAAGTTCC 60.142 45.833 0.00 0.00 35.00 3.62
1949 2431 2.705658 CCATATAAGTGAGGGCAGTCCA 59.294 50.000 0.00 0.00 38.24 4.02
2004 2560 2.154462 ACCTTTTCCTTGATGTGAGCG 58.846 47.619 0.00 0.00 0.00 5.03
2198 2906 9.629878 TCTGGAAGGTAACATTGTTTTTAGTAA 57.370 29.630 7.45 0.00 41.41 2.24
2204 2912 9.108284 CAATTTTCTGGAAGGTAACATTGTTTT 57.892 29.630 7.45 0.00 41.41 2.43
2229 2955 1.066303 GAAAAACACATGGGCACGACA 59.934 47.619 0.00 0.00 0.00 4.35
2230 2956 1.336755 AGAAAAACACATGGGCACGAC 59.663 47.619 0.00 0.00 0.00 4.34
2235 2961 5.195001 TCTTGTTAGAAAAACACATGGGC 57.805 39.130 0.00 0.00 0.00 5.36
2294 3020 6.832384 TGTACTCGTCCATAGATTTAGAAGGT 59.168 38.462 0.00 0.00 0.00 3.50
2389 3149 3.518303 AGCGTTTGATCCTAGGTAAAGGT 59.482 43.478 9.08 4.88 37.91 3.50
2394 3154 4.811969 TCAAAGCGTTTGATCCTAGGTA 57.188 40.909 9.08 0.00 44.21 3.08
2436 3212 9.634021 AAAAGTTTATGGGAAATAAAAGGCAAA 57.366 25.926 0.00 0.00 0.00 3.68
2447 3223 8.301002 CGGAATAAGTGAAAAGTTTATGGGAAA 58.699 33.333 0.00 0.00 0.00 3.13
2455 3231 4.149598 AGCCCGGAATAAGTGAAAAGTTT 58.850 39.130 0.73 0.00 0.00 2.66
2457 3233 3.344515 GAGCCCGGAATAAGTGAAAAGT 58.655 45.455 0.73 0.00 0.00 2.66
2458 3234 2.683362 GGAGCCCGGAATAAGTGAAAAG 59.317 50.000 0.73 0.00 0.00 2.27
2459 3235 2.718563 GGAGCCCGGAATAAGTGAAAA 58.281 47.619 0.73 0.00 0.00 2.29
2460 3236 1.406341 CGGAGCCCGGAATAAGTGAAA 60.406 52.381 0.73 0.00 44.15 2.69
2461 3237 0.177141 CGGAGCCCGGAATAAGTGAA 59.823 55.000 0.73 0.00 44.15 3.18
2463 3239 4.438346 CGGAGCCCGGAATAAGTG 57.562 61.111 0.73 0.00 44.15 3.16
2490 3268 4.522789 GGGGAAATAAAGTGAAAGTGCTCA 59.477 41.667 0.00 0.00 0.00 4.26
2492 3270 4.740902 AGGGGAAATAAAGTGAAAGTGCT 58.259 39.130 0.00 0.00 0.00 4.40
2493 3271 5.243954 AGAAGGGGAAATAAAGTGAAAGTGC 59.756 40.000 0.00 0.00 0.00 4.40
2495 3273 6.373759 ACAGAAGGGGAAATAAAGTGAAAGT 58.626 36.000 0.00 0.00 0.00 2.66
2496 3274 6.901081 ACAGAAGGGGAAATAAAGTGAAAG 57.099 37.500 0.00 0.00 0.00 2.62
2497 3275 8.802267 CAATACAGAAGGGGAAATAAAGTGAAA 58.198 33.333 0.00 0.00 0.00 2.69
2511 3289 4.487714 TTAGCCACTCAATACAGAAGGG 57.512 45.455 0.00 0.00 0.00 3.95
2524 3302 2.614829 ATCGCCGTTATTTAGCCACT 57.385 45.000 0.00 0.00 0.00 4.00
2606 3859 2.620115 ACGTCGAAAGTTGACCAGAGTA 59.380 45.455 0.00 0.00 32.68 2.59
2609 3862 2.589798 AACGTCGAAAGTTGACCAGA 57.410 45.000 0.00 0.00 32.68 3.86
2617 3900 2.251642 GGGCAGCAACGTCGAAAGT 61.252 57.895 0.00 0.00 0.00 2.66
2636 3919 2.025155 GACCAGAGAAGGCGAGTCATA 58.975 52.381 0.00 0.00 0.00 2.15
2644 3927 5.491982 TCATCTTTTAAGACCAGAGAAGGC 58.508 41.667 0.00 0.00 37.98 4.35
2704 3987 1.079127 CCGGTTCTGATTCGTGGCT 60.079 57.895 0.00 0.00 0.00 4.75
2779 4062 7.038048 ACTAATACTCACTTAAACTTACCGGC 58.962 38.462 0.00 0.00 0.00 6.13
2781 4064 9.630098 TGAACTAATACTCACTTAAACTTACCG 57.370 33.333 0.00 0.00 0.00 4.02
2808 4093 1.502231 GCGAGCAATCGATACCACAT 58.498 50.000 0.00 0.00 34.64 3.21
2936 4222 3.687698 TGATCAGTGTCATGATTGCACAG 59.312 43.478 15.10 8.75 40.02 3.66
2960 4246 9.537192 CCTACAAACACGTCTTATATTTGGATA 57.463 33.333 0.00 0.00 35.12 2.59
2961 4247 7.012044 GCCTACAAACACGTCTTATATTTGGAT 59.988 37.037 0.00 0.00 35.12 3.41
2962 4248 6.314400 GCCTACAAACACGTCTTATATTTGGA 59.686 38.462 0.00 0.00 35.12 3.53
2976 4272 8.220755 TCCATATCAAATTAGCCTACAAACAC 57.779 34.615 0.00 0.00 0.00 3.32
2986 4282 6.120507 AGAGTCCCTCCATATCAAATTAGC 57.879 41.667 0.00 0.00 0.00 3.09
2998 4294 7.939781 AGGAAAAATAAAATAGAGTCCCTCCA 58.060 34.615 0.00 0.00 0.00 3.86
3026 4322 9.409312 TGCAATGTACATCTAATGAAAAACAAG 57.591 29.630 9.23 0.00 0.00 3.16
3034 4330 5.406477 GCTCGATGCAATGTACATCTAATGA 59.594 40.000 9.23 3.04 41.45 2.57
3048 4344 6.795098 TTTTAAGAAAGTAGCTCGATGCAA 57.205 33.333 9.09 0.00 45.94 4.08
3050 4346 6.520104 GTGTTTTTAAGAAAGTAGCTCGATGC 59.480 38.462 0.00 0.00 43.29 3.91
3056 4352 8.618677 GGTAAGTGTGTTTTTAAGAAAGTAGCT 58.381 33.333 0.00 0.00 0.00 3.32
3073 4369 4.180817 TCATAGTCGCATTGGTAAGTGTG 58.819 43.478 0.00 0.00 0.00 3.82
3079 4377 3.728076 GACCTCATAGTCGCATTGGTA 57.272 47.619 0.00 0.00 0.00 3.25
3093 4391 2.211250 ACCTTACTAGTGCGACCTCA 57.789 50.000 5.39 0.00 0.00 3.86
3095 4393 2.373224 GGTACCTTACTAGTGCGACCT 58.627 52.381 5.39 0.00 0.00 3.85
3111 4409 2.158928 TGTGGGTAATATGCACGGGTAC 60.159 50.000 0.00 0.00 0.00 3.34
3112 4410 2.117051 TGTGGGTAATATGCACGGGTA 58.883 47.619 0.00 0.00 0.00 3.69
3113 4411 0.913205 TGTGGGTAATATGCACGGGT 59.087 50.000 0.00 0.00 0.00 5.28
3114 4412 2.045561 TTGTGGGTAATATGCACGGG 57.954 50.000 0.00 0.00 0.00 5.28
3115 4413 4.647424 ATTTTGTGGGTAATATGCACGG 57.353 40.909 0.00 0.00 0.00 4.94
3116 4414 5.066634 TGGTATTTTGTGGGTAATATGCACG 59.933 40.000 0.00 0.00 0.00 5.34
3117 4415 6.458232 TGGTATTTTGTGGGTAATATGCAC 57.542 37.500 0.00 0.00 0.00 4.57
3118 4416 6.836007 TGATGGTATTTTGTGGGTAATATGCA 59.164 34.615 0.00 0.00 0.00 3.96
3119 4417 7.145323 GTGATGGTATTTTGTGGGTAATATGC 58.855 38.462 0.00 0.00 0.00 3.14
3120 4418 7.286546 TGGTGATGGTATTTTGTGGGTAATATG 59.713 37.037 0.00 0.00 0.00 1.78
3121 4419 7.358263 TGGTGATGGTATTTTGTGGGTAATAT 58.642 34.615 0.00 0.00 0.00 1.28
3122 4420 6.732487 TGGTGATGGTATTTTGTGGGTAATA 58.268 36.000 0.00 0.00 0.00 0.98
3123 4421 5.584913 TGGTGATGGTATTTTGTGGGTAAT 58.415 37.500 0.00 0.00 0.00 1.89
3124 4422 4.999310 TGGTGATGGTATTTTGTGGGTAA 58.001 39.130 0.00 0.00 0.00 2.85
3125 4423 4.659529 TGGTGATGGTATTTTGTGGGTA 57.340 40.909 0.00 0.00 0.00 3.69
3126 4424 3.534357 TGGTGATGGTATTTTGTGGGT 57.466 42.857 0.00 0.00 0.00 4.51
3127 4425 4.465660 TGAATGGTGATGGTATTTTGTGGG 59.534 41.667 0.00 0.00 0.00 4.61
3128 4426 5.653507 CTGAATGGTGATGGTATTTTGTGG 58.346 41.667 0.00 0.00 0.00 4.17
3129 4427 5.104374 GCTGAATGGTGATGGTATTTTGTG 58.896 41.667 0.00 0.00 0.00 3.33
3130 4428 4.771577 TGCTGAATGGTGATGGTATTTTGT 59.228 37.500 0.00 0.00 0.00 2.83
3131 4429 5.327616 TGCTGAATGGTGATGGTATTTTG 57.672 39.130 0.00 0.00 0.00 2.44
3132 4430 5.999205 TTGCTGAATGGTGATGGTATTTT 57.001 34.783 0.00 0.00 0.00 1.82
3133 4431 7.844493 ATATTGCTGAATGGTGATGGTATTT 57.156 32.000 0.00 0.00 0.00 1.40
3134 4432 7.844493 AATATTGCTGAATGGTGATGGTATT 57.156 32.000 0.00 0.00 0.00 1.89
3135 4433 7.844493 AAATATTGCTGAATGGTGATGGTAT 57.156 32.000 0.00 0.00 0.00 2.73
3136 4434 7.777440 TGTAAATATTGCTGAATGGTGATGGTA 59.223 33.333 0.00 0.00 0.00 3.25
3137 4435 6.606796 TGTAAATATTGCTGAATGGTGATGGT 59.393 34.615 0.00 0.00 0.00 3.55
3138 4436 7.013559 TCTGTAAATATTGCTGAATGGTGATGG 59.986 37.037 0.00 0.00 0.00 3.51
3139 4437 7.859377 GTCTGTAAATATTGCTGAATGGTGATG 59.141 37.037 0.00 0.00 0.00 3.07
3140 4438 7.776969 AGTCTGTAAATATTGCTGAATGGTGAT 59.223 33.333 0.00 0.00 0.00 3.06
3141 4439 7.112122 AGTCTGTAAATATTGCTGAATGGTGA 58.888 34.615 0.00 0.00 0.00 4.02
3142 4440 7.281774 AGAGTCTGTAAATATTGCTGAATGGTG 59.718 37.037 0.00 0.00 0.00 4.17
3143 4441 7.341805 AGAGTCTGTAAATATTGCTGAATGGT 58.658 34.615 0.00 0.00 0.00 3.55
3144 4442 7.798596 AGAGTCTGTAAATATTGCTGAATGG 57.201 36.000 0.00 0.00 0.00 3.16
3160 4458 7.863375 GCTCGATTTGTACAATATAGAGTCTGT 59.137 37.037 24.18 0.00 0.00 3.41
3161 4459 8.079203 AGCTCGATTTGTACAATATAGAGTCTG 58.921 37.037 24.18 12.58 0.00 3.51
3162 4460 8.172352 AGCTCGATTTGTACAATATAGAGTCT 57.828 34.615 24.18 20.82 0.00 3.24
3163 4461 8.804688 AAGCTCGATTTGTACAATATAGAGTC 57.195 34.615 24.18 19.83 0.00 3.36
3164 4462 8.414003 TGAAGCTCGATTTGTACAATATAGAGT 58.586 33.333 24.18 15.21 0.00 3.24
3165 4463 8.803201 TGAAGCTCGATTTGTACAATATAGAG 57.197 34.615 21.98 21.98 0.00 2.43
3166 4464 9.764363 AATGAAGCTCGATTTGTACAATATAGA 57.236 29.630 9.56 10.26 0.00 1.98
3169 4467 8.892723 TCAAATGAAGCTCGATTTGTACAATAT 58.107 29.630 21.22 6.09 39.54 1.28
3170 4468 8.262715 TCAAATGAAGCTCGATTTGTACAATA 57.737 30.769 21.22 1.09 39.54 1.90
3171 4469 7.144722 TCAAATGAAGCTCGATTTGTACAAT 57.855 32.000 21.22 0.00 39.54 2.71
3172 4470 6.552859 TCAAATGAAGCTCGATTTGTACAA 57.447 33.333 21.22 3.59 39.54 2.41
3173 4471 6.741992 ATCAAATGAAGCTCGATTTGTACA 57.258 33.333 21.22 0.00 39.54 2.90
3174 4472 8.452989 AAAATCAAATGAAGCTCGATTTGTAC 57.547 30.769 21.22 0.00 39.54 2.90
3176 4474 9.294030 GATAAAATCAAATGAAGCTCGATTTGT 57.706 29.630 21.22 11.70 39.54 2.83
3177 4475 8.466799 CGATAAAATCAAATGAAGCTCGATTTG 58.533 33.333 18.16 18.16 39.79 2.32
3178 4476 8.397906 TCGATAAAATCAAATGAAGCTCGATTT 58.602 29.630 0.00 0.00 37.78 2.17
3179 4477 7.919690 TCGATAAAATCAAATGAAGCTCGATT 58.080 30.769 0.00 0.00 0.00 3.34
3180 4478 7.482654 TCGATAAAATCAAATGAAGCTCGAT 57.517 32.000 0.00 0.00 0.00 3.59
3181 4479 6.902224 TCGATAAAATCAAATGAAGCTCGA 57.098 33.333 0.00 0.00 0.00 4.04
3182 4480 9.310971 CTTATCGATAAAATCAAATGAAGCTCG 57.689 33.333 18.08 0.00 0.00 5.03
3197 4495 9.419297 CCGAACCATCTATTTCTTATCGATAAA 57.581 33.333 18.08 6.79 0.00 1.40
3198 4496 8.582437 ACCGAACCATCTATTTCTTATCGATAA 58.418 33.333 16.69 16.69 0.00 1.75
3199 4497 8.118976 ACCGAACCATCTATTTCTTATCGATA 57.881 34.615 0.00 0.00 0.00 2.92
3200 4498 6.994221 ACCGAACCATCTATTTCTTATCGAT 58.006 36.000 2.16 2.16 0.00 3.59
3201 4499 6.401047 ACCGAACCATCTATTTCTTATCGA 57.599 37.500 0.00 0.00 0.00 3.59
3202 4500 7.328737 CCTAACCGAACCATCTATTTCTTATCG 59.671 40.741 0.00 0.00 0.00 2.92
3203 4501 8.148999 ACCTAACCGAACCATCTATTTCTTATC 58.851 37.037 0.00 0.00 0.00 1.75
3204 4502 8.030913 ACCTAACCGAACCATCTATTTCTTAT 57.969 34.615 0.00 0.00 0.00 1.73
3205 4503 7.427989 ACCTAACCGAACCATCTATTTCTTA 57.572 36.000 0.00 0.00 0.00 2.10
3206 4504 6.309389 ACCTAACCGAACCATCTATTTCTT 57.691 37.500 0.00 0.00 0.00 2.52
3207 4505 5.952347 ACCTAACCGAACCATCTATTTCT 57.048 39.130 0.00 0.00 0.00 2.52
3208 4506 5.878669 ACAACCTAACCGAACCATCTATTTC 59.121 40.000 0.00 0.00 0.00 2.17
3209 4507 5.812286 ACAACCTAACCGAACCATCTATTT 58.188 37.500 0.00 0.00 0.00 1.40
3210 4508 5.431179 ACAACCTAACCGAACCATCTATT 57.569 39.130 0.00 0.00 0.00 1.73
3211 4509 5.046159 TCAACAACCTAACCGAACCATCTAT 60.046 40.000 0.00 0.00 0.00 1.98
3212 4510 4.283978 TCAACAACCTAACCGAACCATCTA 59.716 41.667 0.00 0.00 0.00 1.98
3213 4511 3.071892 TCAACAACCTAACCGAACCATCT 59.928 43.478 0.00 0.00 0.00 2.90
3214 4512 3.404899 TCAACAACCTAACCGAACCATC 58.595 45.455 0.00 0.00 0.00 3.51
3215 4513 3.495434 TCAACAACCTAACCGAACCAT 57.505 42.857 0.00 0.00 0.00 3.55
3216 4514 3.207778 CTTCAACAACCTAACCGAACCA 58.792 45.455 0.00 0.00 0.00 3.67
3217 4515 3.208594 ACTTCAACAACCTAACCGAACC 58.791 45.455 0.00 0.00 0.00 3.62
3218 4516 4.124970 AGACTTCAACAACCTAACCGAAC 58.875 43.478 0.00 0.00 0.00 3.95
3219 4517 4.411256 AGACTTCAACAACCTAACCGAA 57.589 40.909 0.00 0.00 0.00 4.30
3220 4518 4.828939 TCTAGACTTCAACAACCTAACCGA 59.171 41.667 0.00 0.00 0.00 4.69
3221 4519 5.130292 TCTAGACTTCAACAACCTAACCG 57.870 43.478 0.00 0.00 0.00 4.44
3222 4520 6.107343 GGATCTAGACTTCAACAACCTAACC 58.893 44.000 0.00 0.00 0.00 2.85
3223 4521 6.070710 AGGGATCTAGACTTCAACAACCTAAC 60.071 42.308 0.00 0.00 0.00 2.34
3224 4522 6.023603 AGGGATCTAGACTTCAACAACCTAA 58.976 40.000 0.00 0.00 0.00 2.69
3225 4523 5.590818 AGGGATCTAGACTTCAACAACCTA 58.409 41.667 0.00 0.00 0.00 3.08
3226 4524 4.430441 AGGGATCTAGACTTCAACAACCT 58.570 43.478 0.00 0.00 0.00 3.50
3227 4525 4.828072 AGGGATCTAGACTTCAACAACC 57.172 45.455 0.00 0.00 0.00 3.77
3228 4526 6.981559 GTCATAGGGATCTAGACTTCAACAAC 59.018 42.308 0.00 0.00 0.00 3.32
3229 4527 6.667848 TGTCATAGGGATCTAGACTTCAACAA 59.332 38.462 0.00 0.00 31.25 2.83
3230 4528 6.096987 GTGTCATAGGGATCTAGACTTCAACA 59.903 42.308 0.00 0.00 31.25 3.33
3231 4529 6.461788 GGTGTCATAGGGATCTAGACTTCAAC 60.462 46.154 0.00 0.00 31.25 3.18
3232 4530 5.598830 GGTGTCATAGGGATCTAGACTTCAA 59.401 44.000 0.00 0.00 31.25 2.69
3233 4531 5.103473 AGGTGTCATAGGGATCTAGACTTCA 60.103 44.000 0.00 0.00 31.25 3.02
3234 4532 5.390387 AGGTGTCATAGGGATCTAGACTTC 58.610 45.833 0.00 0.00 31.25 3.01
3235 4533 5.411103 AGGTGTCATAGGGATCTAGACTT 57.589 43.478 0.00 0.00 31.25 3.01
3236 4534 5.135362 AGAAGGTGTCATAGGGATCTAGACT 59.865 44.000 0.00 0.00 31.25 3.24
3237 4535 5.390387 AGAAGGTGTCATAGGGATCTAGAC 58.610 45.833 0.00 0.00 0.00 2.59
3238 4536 5.671463 AGAAGGTGTCATAGGGATCTAGA 57.329 43.478 0.00 0.00 0.00 2.43
3239 4537 6.307776 TGTAGAAGGTGTCATAGGGATCTAG 58.692 44.000 0.00 0.00 0.00 2.43
3240 4538 6.102762 TCTGTAGAAGGTGTCATAGGGATCTA 59.897 42.308 0.00 0.00 0.00 1.98
3241 4539 5.103473 TCTGTAGAAGGTGTCATAGGGATCT 60.103 44.000 0.00 0.00 0.00 2.75
3242 4540 5.010213 GTCTGTAGAAGGTGTCATAGGGATC 59.990 48.000 0.00 0.00 0.00 3.36
3243 4541 4.896482 GTCTGTAGAAGGTGTCATAGGGAT 59.104 45.833 0.00 0.00 0.00 3.85
3244 4542 4.279145 GTCTGTAGAAGGTGTCATAGGGA 58.721 47.826 0.00 0.00 0.00 4.20
3245 4543 3.385111 GGTCTGTAGAAGGTGTCATAGGG 59.615 52.174 0.00 0.00 0.00 3.53
3246 4544 3.066900 CGGTCTGTAGAAGGTGTCATAGG 59.933 52.174 0.00 0.00 0.00 2.57
3247 4545 3.066900 CCGGTCTGTAGAAGGTGTCATAG 59.933 52.174 0.00 0.00 0.00 2.23
3248 4546 3.021695 CCGGTCTGTAGAAGGTGTCATA 58.978 50.000 0.00 0.00 0.00 2.15
3249 4547 1.825474 CCGGTCTGTAGAAGGTGTCAT 59.175 52.381 0.00 0.00 0.00 3.06
3250 4548 1.202964 TCCGGTCTGTAGAAGGTGTCA 60.203 52.381 0.00 0.00 0.00 3.58
3251 4549 1.542492 TCCGGTCTGTAGAAGGTGTC 58.458 55.000 0.00 0.00 0.00 3.67
3252 4550 2.100989 GATCCGGTCTGTAGAAGGTGT 58.899 52.381 0.00 0.00 0.00 4.16
3253 4551 1.409427 GGATCCGGTCTGTAGAAGGTG 59.591 57.143 0.00 0.00 0.00 4.00
3254 4552 1.288335 AGGATCCGGTCTGTAGAAGGT 59.712 52.381 5.98 0.00 0.00 3.50
3255 4553 2.074729 AGGATCCGGTCTGTAGAAGG 57.925 55.000 5.98 0.00 0.00 3.46
3256 4554 4.399219 TGATAGGATCCGGTCTGTAGAAG 58.601 47.826 16.97 0.00 0.00 2.85
3257 4555 4.448720 TGATAGGATCCGGTCTGTAGAA 57.551 45.455 16.97 0.00 0.00 2.10
3258 4556 4.142790 GTTGATAGGATCCGGTCTGTAGA 58.857 47.826 16.97 0.00 0.00 2.59
3259 4557 3.256136 GGTTGATAGGATCCGGTCTGTAG 59.744 52.174 16.97 0.00 0.00 2.74
3260 4558 3.228453 GGTTGATAGGATCCGGTCTGTA 58.772 50.000 16.97 0.57 0.00 2.74
3261 4559 2.040178 GGTTGATAGGATCCGGTCTGT 58.960 52.381 16.97 0.00 0.00 3.41
3262 4560 1.344763 GGGTTGATAGGATCCGGTCTG 59.655 57.143 16.97 0.00 0.00 3.51
3263 4561 1.718280 GGGTTGATAGGATCCGGTCT 58.282 55.000 16.97 0.25 0.00 3.85
3264 4562 0.685660 GGGGTTGATAGGATCCGGTC 59.314 60.000 5.98 9.20 0.00 4.79
3265 4563 0.030501 TGGGGTTGATAGGATCCGGT 60.031 55.000 5.98 0.00 0.00 5.28
3266 4564 1.136828 TTGGGGTTGATAGGATCCGG 58.863 55.000 5.98 0.00 0.00 5.14
3267 4565 2.371841 TGATTGGGGTTGATAGGATCCG 59.628 50.000 5.98 0.00 0.00 4.18
3268 4566 4.338879 CATGATTGGGGTTGATAGGATCC 58.661 47.826 2.48 2.48 0.00 3.36
3269 4567 4.338879 CCATGATTGGGGTTGATAGGATC 58.661 47.826 0.00 0.00 39.56 3.36
3270 4568 3.501019 GCCATGATTGGGGTTGATAGGAT 60.501 47.826 0.00 0.00 43.84 3.24
3271 4569 2.158475 GCCATGATTGGGGTTGATAGGA 60.158 50.000 0.00 0.00 43.84 2.94
3272 4570 2.242043 GCCATGATTGGGGTTGATAGG 58.758 52.381 0.00 0.00 43.84 2.57
3273 4571 2.242043 GGCCATGATTGGGGTTGATAG 58.758 52.381 0.00 0.00 43.84 2.08
3274 4572 1.572895 TGGCCATGATTGGGGTTGATA 59.427 47.619 0.00 0.00 43.84 2.15
3275 4573 0.339162 TGGCCATGATTGGGGTTGAT 59.661 50.000 0.00 0.00 43.84 2.57
3276 4574 0.339162 ATGGCCATGATTGGGGTTGA 59.661 50.000 20.04 0.00 43.84 3.18
3277 4575 0.466543 CATGGCCATGATTGGGGTTG 59.533 55.000 37.84 10.72 43.84 3.77
3278 4576 0.691748 CCATGGCCATGATTGGGGTT 60.692 55.000 41.32 4.59 43.84 4.11
3279 4577 1.075076 CCATGGCCATGATTGGGGT 60.075 57.895 41.32 5.46 43.84 4.95
3280 4578 1.117142 GTCCATGGCCATGATTGGGG 61.117 60.000 41.32 26.16 43.84 4.96
3281 4579 0.105862 AGTCCATGGCCATGATTGGG 60.106 55.000 41.32 26.86 43.84 4.12
3282 4580 1.411246 CAAGTCCATGGCCATGATTGG 59.589 52.381 41.32 29.02 46.66 3.16
3283 4581 2.882927 CAAGTCCATGGCCATGATTG 57.117 50.000 41.32 33.65 41.20 2.67


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.